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- PDB-1le9: Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti -

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Basic information

Entry
Database: PDB / ID: 1le9
TitleCrystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti
Components
  • 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'
  • 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'
  • NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT
  • NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
KeywordsTRANSCRIPTION/DNA / transcription factor / NF-kB-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / mammary gland involution / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / antibacterial innate immune response / prolactin signaling pathway / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / response to cobalamin / cellular response to peptidoglycan / positive regulation of lipid storage / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / negative regulation of cytokine production / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / positive regulation of vascular endothelial growth factor production / cellular response to angiotensin / general transcription initiation factor binding / response to cAMP / canonical NF-kappaB signal transduction / positive regulation of cholesterol efflux / hair follicle development / NF-kappaB binding / positive regulation of transcription initiation by RNA polymerase II / lymph node development / neuropeptide signaling pathway / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / JNK cascade / response to muscle stretch / Neutrophil degranulation / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / negative regulation of insulin receptor signaling pathway / response to progesterone / negative regulation of miRNA transcription / negative regulation of angiogenesis / animal organ morphogenesis / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / B cell receptor signaling pathway / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / liver development / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / defense response / response to insulin / negative regulation of protein catabolic process
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain ...Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBenjamin, B. / Huang, D.B. / Chen-Park, F.E. / Sigler, P.B. / Ghosh, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site.
Authors: Berkowitz, B. / Huang, D.B. / Chen-Park, F.E. / Sigler, P.B. / Ghosh, G.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'
D: 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'
G: 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'
H: 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'
A: NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
B: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT
E: NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
F: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)146,9928
Polymers146,9928
Non-polymers00
Water00
1
C: 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'
D: 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'
A: NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
B: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)73,4964
Polymers73,4964
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'
H: 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'
E: NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
F: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)73,4964
Polymers73,4964
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.835, 138.002, 90.044
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'


Mass: 3644.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Ig/HIV2-kB DNA
#2: DNA chain 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'


Mass: 3680.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Ig/HIV2-kB DNA
#3: Protein NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT / NF-KB P65


Mass: 31115.236 Da / Num. of mol.: 2 / Fragment: p65 RHR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: rela / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04207
#4: Protein NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT / NF-KB P50


Mass: 35056.066 Da / Num. of mol.: 2 / Fragment: p50 RHR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: nfkb1 / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25799
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2CaCl211
3Na(C2H3O2)11
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
250 mMsodium acetate1reservoirpH5.5
350 mM1reservoirCaCl2
40.125 %beta-octyl glucopyranoside1reservoir
51.0 mMspermine1reservoir
610 mMdithiothreitol1reservoir
77-8 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 2, 1999
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 33446 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 98
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 249074
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.434

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKX

1vkx


Resolution: 3→30 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1704 -RANDOM
Rwork0.249 ---
all-31118 --
obs-28493 85.4 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9260 972 0 0 10232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_bond_d0.008
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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